| Variant ID: vg0202540167 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2540167 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.00, others allele: 0.00, population size: 295. )
AAAGACGTCAGATCATATGATGTCAAACAAGTACGCGGTAAGAGTAATTGGTAGATTGGTTTTTTAAATTAATCTACTAATTTCGTAGATACATCCGGCA[T/A]
GTATCTACAAAGGTACGCAATATTTTATATGCAATTTATCATACCTATTCAGATCATACAGAATTGTCAGATCTATAATTTATTATGTTTACCTAGAGCA
TGCTCTAGGTAAACATAATAAATTATAGATCTGACAATTCTGTATGATCTGAATAGGTATGATAAATTGCATATAAAATATTGCGTACCTTTGTAGATAC[A/T]
TGCCGGATGTATCTACGAAATTAGTAGATTAATTTAAAAAACCAATCTACCAATTACTCTTACCGCGTACTTGTTTGACATCATATGATCTGACGTCTTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.80% | 17.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 70.90% | 29.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 60.30% | 39.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 51.80% | 48.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 61.20% | 38.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202540167 | T -> A | LOC_Os02g05270.1 | upstream_gene_variant ; 3992.0bp to feature; MODIFIER | silent_mutation | Average:41.013; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540167 | T -> A | LOC_Os02g05280.1 | downstream_gene_variant ; 1497.0bp to feature; MODIFIER | silent_mutation | Average:41.013; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540167 | T -> A | LOC_Os02g05300.1 | downstream_gene_variant ; 1923.0bp to feature; MODIFIER | silent_mutation | Average:41.013; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg0202540167 | T -> A | LOC_Os02g05290.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.013; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |